Class: LiteralMapping
Represents an individual mapping between a literal and an entity. Note that this schema has been created on 01.08.2023 and is subject to change.
URI: owl:Axiom
classDiagram
class LiteralMapping
LiteralMapping : author_id
LiteralMapping : author_label
LiteralMapping : comment
LiteralMapping : confidence
LiteralMapping : creator_id
LiteralMapping : creator_label
LiteralMapping : license
LiteralMapping : literal
LiteralMapping : literal_datatype
LiteralMapping : literal_preprocessing
LiteralMapping : literal_source
LiteralMapping : literal_source_version
LiteralMapping : mapping_cardinality
LiteralMapping --|> mapping_cardinality_enum : mapping_cardinality
LiteralMapping : mapping_date
LiteralMapping : mapping_justification
LiteralMapping : mapping_provider
LiteralMapping : mapping_source
LiteralMapping : mapping_tool
LiteralMapping : mapping_tool_version
LiteralMapping : match_string
LiteralMapping : object_category
LiteralMapping : object_id
LiteralMapping : object_label
LiteralMapping : object_match_field
LiteralMapping : object_preprocessing
LiteralMapping : object_source
LiteralMapping : object_source_version
LiteralMapping : object_type
LiteralMapping --|> entity_type_enum : object_type
LiteralMapping : other
LiteralMapping : predicate_id
LiteralMapping : predicate_label
LiteralMapping : predicate_modifier
LiteralMapping --|> predicate_modifier_enum : predicate_modifier
LiteralMapping : reviewer_id
LiteralMapping : reviewer_label
LiteralMapping : see_also
LiteralMapping : similarity_measure
LiteralMapping : similarity_score
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
literal | 1..1 String |
The literal being mapped | direct |
literal_datatype | 0..1 Uri |
The datatype of the literal being mapped | direct |
predicate_id | 1..1 EntityReference |
The ID of the predicate or relation that relates the subject and object of th... | direct |
predicate_label | 0..1 String |
The label of the predicate/relation of the mapping | direct |
predicate_modifier | 0..1 PredicateModifierEnum |
A modifier for negating the prediate | direct |
object_id | 1..1 EntityReference |
The ID of the object of the mapping | direct |
object_label | 0..1 recommended String |
The label of object of the mapping | direct |
object_category | 0..1 String |
The conceptual category to which the subject belongs to | direct |
mapping_justification | 1..1 EntityReference |
A mapping justification is an action (or the written representation of that a... | direct |
author_id | 0..* EntityReference |
Identifies the persons or groups responsible for asserting the mappings | direct |
author_label | 0..* String |
A string identifying the author of this mapping | direct |
reviewer_id | 0..* EntityReference |
Identifies the persons or groups that reviewed and confirmed the mapping | direct |
reviewer_label | 0..* String |
A string identifying the reviewer of this mapping | direct |
creator_id | 0..* EntityReference |
Identifies the persons or groups responsible for the creation of the mapping | direct |
creator_label | 0..* String |
A string identifying the creator of this mapping | direct |
license | 0..1 Uri |
A url to the license of the mapping | direct |
literal_source | 0..1 EntityReference |
URI of ontology source for the literal | direct |
literal_source_version | 0..1 String |
Version IRI or version string of the source of the literal | direct |
object_type | 0..1 EntityTypeEnum |
The type of entity that is being mapped | direct |
object_source | 0..1 EntityReference |
URI of vocabulary or identifier source for the object | direct |
object_source_version | 0..1 String |
Version IRI or version string of the source of the object term | direct |
mapping_provider | 0..1 Uri |
URL pointing to the source that provided the mapping, for example an ontology... | direct |
mapping_source | 0..1 EntityReference |
The mapping set this mapping was originally defined in | direct |
mapping_cardinality | 0..1 MappingCardinalityEnum |
A string indicating whether this mapping is from a 1:1 (the subject_id maps t... | direct |
mapping_tool | 0..1 String |
A reference to the tool or algorithm that was used to generate the mapping | direct |
mapping_tool_version | 0..1 String |
Version string that denotes the version of the mapping tool used | direct |
mapping_date | 0..1 Date |
The date the mapping was asserted | direct |
confidence | 0..1 Double |
A score between 0 and 1 to denote the confidence or probability that the matc... | direct |
object_match_field | 0..* EntityReference |
A list of properties (term annotations on the object) that was used for the m... | direct |
match_string | 0..* String |
String that is shared by subj/obj | direct |
literal_preprocessing | 0..* EntityReference |
Method of preprocessing applied to the literal | direct |
object_preprocessing | 0..* EntityReference |
Method of preprocessing applied to the fields of the object | direct |
similarity_score | 0..1 Double |
A score between 0 and 1 to denote the similarity, where 1 denotes equivalence | direct |
similarity_measure | 0..1 String |
The measure used for computing the the similarity score | direct |
see_also | 0..* String |
A URL specific for the mapping instance | direct |
other | 0..1 String |
Pipe separated list of key value pairs for properties not part of the SSSOM s... | direct |
comment | 0..1 String |
Free text field containing either curator notes or text generated by tool pro... | direct |
See Also
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/sssom/schema/
Mappings
Mapping Type | Mapped Value |
---|---|
self | owl:Axiom |
native | sssom:LiteralMapping |
LinkML Source
Direct
name: literal mapping
description: Represents an individual mapping between a literal and an entity. Note
that this schema has been created on 01.08.2023 and is subject to change.
from_schema: https://w3id.org/sssom/schema/
see_also:
- https://mapping-commons.github.io/sssom/sssom-profiles/
slots:
- literal
- literal_datatype
- predicate_id
- predicate_label
- predicate_modifier
- object_id
- object_label
- object_category
- mapping_justification
- author_id
- author_label
- reviewer_id
- reviewer_label
- creator_id
- creator_label
- license
- literal_source
- literal_source_version
- object_type
- object_source
- object_source_version
- mapping_provider
- mapping_source
- mapping_cardinality
- mapping_tool
- mapping_tool_version
- mapping_date
- confidence
- object_match_field
- match_string
- literal_preprocessing
- object_preprocessing
- similarity_score
- similarity_measure
- see_also
- other
- comment
class_uri: owl:Axiom
Induced
name: literal mapping
description: Represents an individual mapping between a literal and an entity. Note
that this schema has been created on 01.08.2023 and is subject to change.
from_schema: https://w3id.org/sssom/schema/
see_also:
- https://mapping-commons.github.io/sssom/sssom-profiles/
attributes:
literal:
name: literal
description: The literal being mapped
examples:
- value: Alzheimer
description: A string referring to some thing.
from_schema: https://w3id.org/sssom/schema/
mappings:
- owl:annotatedSource
rank: 1000
slot_uri: owl:annotatedTarget
alias: literal
owner: literal mapping
domain_of:
- literal mapping
range: string
required: true
literal_datatype:
name: literal_datatype
description: The datatype of the literal being mapped
examples:
- value: xsd:string
description: A string referring to some thing.
from_schema: https://w3id.org/sssom/schema/
mappings:
- rdf:datatype
rank: 1000
slot_uri: rdf:datatype
alias: literal_datatype
owner: literal mapping
domain_of:
- literal mapping
range: uri
required: false
predicate_id:
name: predicate_id
description: The ID of the predicate or relation that relates the subject and
object of this match.
examples:
- value: skos:exactMatch
from_schema: https://w3id.org/sssom/schema/
mappings:
- owl:annotatedProperty
rank: 1000
slot_uri: owl:annotatedProperty
alias: predicate_id
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: EntityReference
required: true
predicate_label:
name: predicate_label
description: The label of the predicate/relation of the mapping
examples:
- value: owl:sameAs
description: The subject and the object are instances (owl individuals), and
the two instances are the same.
- value: owl:equivalentClass
description: The subject and the object are classes (owl class), and the two
classes are the same.
- value: owl:equivalentProperty
description: The subject and the object are properties (owl object, data, annotation
properties), and the two properties are the same.
- value: rdfs:subClassOf
description: The subject and the object are classes (owl class), and the subject
is a subclass of the object.
- value: rdfs:subPropertyOf
description: The subject and the object are properties (owl object, data, annotation
properties), and the subject is a subproperty of the object.
- value: skos:relatedMatch
description: The subject and the object are associated in some unspecified way.
- value: skos:closeMatch
description: The subject and the object are sufficiently similar that they can
be used interchangeably in some information retrieval applications.
- value: skos:exactMatch
description: The subject and the object can, with a high degree of confidence,
be used interchangeably across a wide range of information retrieval applications.
- value: skos:narrowMatch
description: 'From the SKOS primer: A triple skos:narrower (and skos:narrowMatch)
asserts that , the object of the triple, is a narrower concept than , the
subject of the triple.'
- value: skos:broadMatch
description: 'From the SKOS primer: A triple skos:broader (and skos:broadMatch)
asserts that , the object of the triple, is a broader concept than , the subject
of the triple.'
- value: oboInOwl:hasDbXref
description: Two terms are related in some way. The meaning is frequently consistent
across a single set of mappings. Note this property is often overloaded even
where the terms are of a different nature (e.g. interpro2go)
- value: rdfs:seeAlso
description: The subject and the object are associated in some unspecified way.
The object IRI often resolves to a resource on the web that provides additional
information.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: predicate_label
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: string
predicate_modifier:
name: predicate_modifier
description: A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40
for discussion
examples:
- value: Not
description: Negates the predicate, see documentation of predicate_modifier_enum
from_schema: https://w3id.org/sssom/schema/
see_also:
- https://github.com/mapping-commons/sssom/issues/107
rank: 1000
alias: predicate_modifier
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: predicate_modifier_enum
object_id:
name: object_id
description: The ID of the object of the mapping.
examples:
- value: HP:0009894
description: The CURIE denoting the Human Phenotype Ontology concept of 'Thickened
ears'
from_schema: https://w3id.org/sssom/schema/
mappings:
- owl:annotatedTarget
rank: 1000
slot_uri: owl:annotatedTarget
alias: object_id
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: EntityReference
required: true
object_label:
name: object_label
description: The label of object of the mapping
examples:
- value: Thickened ears
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: object_label
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: string
recommended: true
object_category:
name: object_category
description: The conceptual category to which the subject belongs to. This can
be a string denoting the category or a term from a controlled vocabulary. This
slot is deliberately underspecified. Conceptual categories can range from those
that are found in general upper ontologies such as BFO (e.g. process, temporal
region, etc) to those that serve as upper ontologies in specific domains, such
as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this
optional field is documentation for human reviewers - when a category is known
and documented clearly, the cost of interpreting and evaluating the mapping
decreases.
examples:
- value: UBERON:0001062
description: (The CURIE of the Uberon term for "anatomical entity".)
- value: anatomical entity
description: (A string, rather than ID, describing the "anatomical entity" category.
This is possible, but less preferred than using an ID.)
- value: biolink:Gene
description: (The CURIE of the biolink class for genes.)
from_schema: https://w3id.org/sssom/schema/
see_also:
- https://github.com/mapping-commons/sssom/issues/13
- https://github.com/mapping-commons/sssom/issues/256
rank: 1000
alias: object_category
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: string
mapping_justification:
name: mapping_justification
description: A mapping justification is an action (or the written representation
of that action) of showing a mapping to be right or reasonable.
examples:
- value: semapv:LexicalMatching
- value: semapv:ManualMappingCuration
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: mapping_justification
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: EntityReference
required: true
pattern: ^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining)$
any_of:
- equals_string: semapv:LexicalMatching
- equals_string: semapv:LogicalReasoning
- equals_string: semapv:CompositeMatching
- equals_string: semapv:UnspecifiedMatching
- equals_string: semapv:SemanticSimilarityThresholdMatching
- equals_string: semapv:LexicalSimilarityThresholdMatching
- equals_string: semapv:MappingChaining
- equals_string: semapv:MappingReview
- equals_string: semapv:ManualMappingCuration
author_id:
name: author_id
description: Identifies the persons or groups responsible for asserting the mappings.
Recommended to be a list of ORCIDs or otherwise identifying URIs.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
slot_uri: pav:authoredBy
multivalued: true
alias: author_id
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: EntityReference
author_label:
name: author_label
description: A string identifying the author of this mapping. In the spirit of
provenance, consider using author_id instead.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: author_label
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: string
reviewer_id:
name: reviewer_id
description: Identifies the persons or groups that reviewed and confirmed the
mapping. Recommended to be a list of ORCIDs or otherwise identifying URIs.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: reviewer_id
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: EntityReference
reviewer_label:
name: reviewer_label
description: A string identifying the reviewer of this mapping. In the spirit
of provenance, consider using reviewer_id instead.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: reviewer_label
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: string
creator_id:
name: creator_id
description: Identifies the persons or groups responsible for the creation of
the mapping. The creator is the agent that put the mapping in its published
form, which may be different from the author, which is a person that was actively
involved in the assertion of the mapping. Recommended to be a list of ORCIDs
or otherwise identifying URIs.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
slot_uri: dcterms:creator
multivalued: true
alias: creator_id
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: EntityReference
creator_label:
name: creator_label
description: A string identifying the creator of this mapping. In the spirit of
provenance, consider using creator_id instead.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: creator_label
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: string
license:
name: license
description: A url to the license of the mapping. In absence of a license we assume
no license.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
slot_uri: dcterms:license
alias: license
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: uri
literal_source:
name: literal_source
description: URI of ontology source for the literal.
examples:
- value: obo:mondo.owl
description: A persistent OBO CURIE pointing to the latest version of the Mondo
ontology.
- value: wikidata:Q7876491
description: A Wikidata identifier for the Uberon ontology resource.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: literal_source
owner: literal mapping
domain_of:
- literal mapping
range: EntityReference
literal_source_version:
name: literal_source_version
description: Version IRI or version string of the source of the literal.
examples:
- value: http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl
description: (A persistent Version IRI pointing to the Mondo version '2021-01-30')
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: literal_source_version
owner: literal mapping
domain_of:
- literal mapping
range: string
object_type:
name: object_type
description: The type of entity that is being mapped.
examples:
- value: owl:Class
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: object_type
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: entity_type_enum
object_source:
name: object_source
description: URI of vocabulary or identifier source for the object.
examples:
- value: obo:mondo.owl
description: A persistent OBO CURIE pointing to the latest version of the Mondo
ontology.
- value: wikidata:Q7876491
description: A Wikidata identifier for the Uberon ontology resource.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: object_source
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: EntityReference
object_source_version:
name: object_source_version
description: Version IRI or version string of the source of the object term.
examples:
- value: http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl
description: (A persistent Version IRI pointing to the Mondo version '2021-01-30')
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: object_source_version
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: string
mapping_provider:
name: mapping_provider
description: URL pointing to the source that provided the mapping, for example
an ontology that already contains the mappings, or a database from which it
was derived.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: mapping_provider
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: uri
mapping_source:
name: mapping_source
description: The mapping set this mapping was originally defined in. mapping_source
is used for example when merging multiple mapping sets or deriving one mapping
set from another.
examples:
- value: MONDO_MAPPINGS:mondo_exactmatch_ncit.sssom.tsv
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: mapping_source
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: EntityReference
mapping_cardinality:
name: mapping_cardinality
description: A string indicating whether this mapping is from a 1:1 (the subject_id
maps to a single object_id), 1:n (the subject maps to more than one object_id),
n:1, 1:0, 0:1 or n:n group. Note that this is a convenience field that should
be derivable from the mapping set.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: mapping_cardinality
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: mapping_cardinality_enum
mapping_tool:
name: mapping_tool
description: A reference to the tool or algorithm that was used to generate the
mapping. Should be a URL pointing to more info about it, but can be free text.
examples:
- value: https://github.com/AgreementMakerLight/AML-Project
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: mapping_tool
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: string
mapping_tool_version:
name: mapping_tool_version
description: Version string that denotes the version of the mapping tool used.
examples:
- value: v3.2
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: mapping_tool_version
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: string
mapping_date:
name: mapping_date
description: The date the mapping was asserted. This is different from the date
the mapping was published or compiled in a SSSOM file.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
slot_uri: pav:authoredOn
alias: mapping_date
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: date
confidence:
name: confidence
description: A score between 0 and 1 to denote the confidence or probability that
the match is correct, where 1 denotes total confidence.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: confidence
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: double
object_match_field:
name: object_match_field
description: A list of properties (term annotations on the object) that was used
for the match.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: object_match_field
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: EntityReference
match_string:
name: match_string
description: String that is shared by subj/obj. It is recommended to indicate
the fields for the match using the object and subject_match_field slots.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: match_string
owner: literal mapping
domain_of:
- mapping
- literal mapping
range: string
literal_preprocessing:
name: literal_preprocessing
description: Method of preprocessing applied to the literal.
examples:
- value: semapv:Stemming
- value: semapv:StopWordRemoval
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: literal_preprocessing
owner: literal mapping
domain_of:
- literal mapping
range: EntityReference
object_preprocessing:
name: object_preprocessing
description: Method of preprocessing applied to the fields of the object. If different
preprocessing steps were performed on different fields, it is recommended to
store the match in separate rows.
examples:
- value: semapv:Stemming
- value: semapv:StopWordRemoval
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: object_preprocessing
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: EntityReference
similarity_score:
name: similarity_score
description: A score between 0 and 1 to denote the similarity, where 1 denotes
equivalence.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: similarity_score
owner: literal mapping
domain_of:
- literal mapping
range: double
similarity_measure:
name: similarity_measure
description: The measure used for computing the the similarity score. To make
processing this field as unambiguous as possible, we recommend using wikidata
identifiers, but wikipedia pages could also be acceptable.
examples:
- value: https://www.wikidata.org/wiki/Q865360
description: (the Wikidata identifier for the Jaccard index measure).
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: similarity_measure
owner: literal mapping
domain_of:
- literal mapping
range: string
see_also:
name: see_also
description: A URL specific for the mapping instance. E.g. for kboom we have a
per-mapping image that shows surrounding axioms that drive probability. Could
also be a github issue URL that discussed a complicated alignment
from_schema: https://w3id.org/sssom/schema/
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
alias: see_also
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: string
other:
name: other
description: Pipe separated list of key value pairs for properties not part of
the SSSOM spec. Can be used to encode additional provenance data.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
alias: other
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: string
comment:
name: comment
description: Free text field containing either curator notes or text generated
by tool providing additional informative information.
from_schema: https://w3id.org/sssom/schema/
rank: 1000
slot_uri: rdfs:comment
alias: comment
owner: literal mapping
domain_of:
- mapping set
- mapping
- literal mapping
range: string
class_uri: owl:Axiom